The ubiquitin-proteasome system UPS is a crucial cellular pathway responsible for the selective degradation of proteins, which contributes to protein turnover, regulation of cellular processes, and removal of damaged or misfolded proteins. The UPS consists of two main components: ubiquitin, a small protein that serves as a molecular tag, and the proteasome, a large protein complex that degrades the tagged proteins. The process involves several steps and regulatory factors, which are outlined below:1. Ubiquitination: The first step in the UPS is the covalent attachment of ubiquitin molecules to the target protein. This process is carried out by a series of enzymes: ubiquitin-activating enzyme E1 , ubiquitin-conjugating enzyme E2 , and ubiquitin ligase E3 . The E1 enzyme activates ubiquitin in an ATP-dependent manner and transfers it to the E2 enzyme. The E3 ligase then recognizes the target protein and facilitates the transfer of ubiquitin from E2 to the target protein, forming an isopeptide bond between the ubiquitin's C-terminus and the target protein's lysine residue. This process can be repeated, leading to the formation of a polyubiquitin chain on the target protein.2. Recognition and binding: The polyubiquitinated protein is then recognized by the proteasome, a large multi-subunit complex with proteolytic activity. The 26S proteasome is the most common form in eukaryotic cells and consists of a 20S core particle and one or two 19S regulatory particles. The 19S regulatory particle recognizes the polyubiquitin chain on the target protein and binds to it.3. Deubiquitination and unfolding: Before degradation, the polyubiquitin chain is removed from the target protein by deubiquitinating enzymes DUBs associated with the 19S regulatory particle. The target protein is then unfolded by ATP-dependent chaperone-like proteins, also part of the 19S regulatory particle, to facilitate its entry into the 20S core particle.4. Proteolysis: The unfolded target protein is translocated into the 20S core particle, where it is degraded by proteolytic enzymes called proteases. The 20S core particle contains multiple proteases with different substrate specificities, ensuring the complete degradation of the target protein into small peptides.5. Recycling: The resulting peptides are released from the proteasome and can be further degraded into amino acids by cytosolic peptidases. The ubiquitin molecules and the proteasome components are recycled for further rounds of protein degradation.The UPS is regulated at multiple levels to ensure the selective degradation of proteins and maintain cellular homeostasis. Some of the regulatory factors include:- Substrate specificity: E3 ubiquitin ligases play a critical role in determining substrate specificity, as they recognize and bind to specific target proteins. There are hundreds of E3 ligases in cells, each with distinct substrate preferences.- Post-translational modifications: The activity of the UPS can be modulated by post-translational modifications, such as phosphorylation, acetylation, or neddylation, which can affect the activity of E1, E2, E3 enzymes, or proteasome components.- Cellular localization: The UPS components can be localized to specific cellular compartments, such as the nucleus, endoplasmic reticulum, or mitochondria, to regulate protein degradation in a spatially controlled manner.- Proteasome assembly and disassembly: The assembly of the 26S proteasome can be regulated by specific assembly chaperones, while its disassembly can be induced under certain conditions, such as oxidative stress or nutrient deprivation.- UPS-associated proteins: Several proteins, such as ubiquitin-like proteins, proteasome-interacting proteins, or proteasome inhibitors, can modulate the UPS activity by interacting with its components.In summary, the ubiquitin-proteasome system is a highly regulated and efficient pathway for protein turnover and degradation in cells. It plays a crucial role in maintaining cellular homeostasis, controlling the levels of regulatory proteins, and eliminating damaged or misfolded proteins.